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// =============================================================== //
// //
// File : seq.cxx //
// Purpose : //
// //
// =============================================================== //
#include "seq.h"
#include "ali.h"
#include "reader.h"
void Seq::out(Writer& write, Format outType) const {
ca_assert(outType == EMBL || outType == GENBANK); // others not implemented yet
const char *sequence = get_seq();
int indk = 1;
for (int indi = 0, indj = 0; indi < get_len(); indi++) {
if ((indk % 60) == 1) {
switch (outType) {
case EMBL: write.out(" "); break;
case GENBANK: write.outf(" %6d ", indk); break;
default: ca_assert(0); break;
}
}
write.out(sequence[indi]);
indj++;
// blank space follows every 10 bases, but not before '\n'
if ((indk % 60) == 0) {
write.out('\n');
indj = 0;
}
else if (indj == 10 && indi != (get_len() - 1)) {
write.out(' ');
indj = 0;
}
indk++;
}
if ((indk % 60) != 1)
write.out('\n');
write.out("//\n");
}
void read_alignment(Alignment& ali, const FormattedFile& in) {
FormatReaderPtr reader = FormatReader::create(in);
while (1) {
SeqPtr seq = new Seq;
if (!reader->read_one_entry(*seq)) break;
ali.add(seq);
}
}
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